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Read and tidy a FASTA file

Source: R/locatePTM.R
tidyFasta.Rd

tidyFasta reads and tidys FASTA file. Use this function as the first step in identifying modification sites.

Usage

tidyFasta(path)

Arguments

path

A string of path to a FASTA file.

Value

A data.table with columns named header, sequence, uniprot_ac, uniprot_iso, entry_name.

Examples

tidyFasta(system.file("extdata", "O13297.fasta", package="MSstatsPTM"))
#>                                                                                                                                        header
#>                                                                                                                                        <char>
#> 1: sp|O13297|CET1_YEAST mRNA-capping enzyme subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=CET1 PE=1 SV=2
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 sequence
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <char>
#> 1: MSYTDNPPQTKRALSLDDLVNHDENEKVKLQKLSEAANGSRPFAENLESDINQTETGQAAPIDNYKESTGHGSHSQKPKSRKSSNDDEETDTDDEMGASGEINFDSEMDFDYDKQHRNLLSNGSPPMNDGSDANAKLEKPSDDSIHQNSKSDEEQRIPKQGNEGNIASNYITQVPLQKQKQTEKKIAGNAVGSVVKKEEEANAAVDNIFEEKATLQSKKNNIKRDLEVLNEISASSKPSKYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM
#>    uniprot_ac uniprot_iso entry_name
#>        <char>      <char>     <char>
#> 1:     O13297      O13297 CET1_YEAST